[gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
question, I have no charges in systems on any atoms. So the extra DOF do
not effect on potential.


Best regards


On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Potential energy is a function of configuration. You can expect the same LJ
> energy if you compare the same configuration, ie that the distribution of
> states is identical. But if you would have the same total energy and a
> different distribution between PE and KE (because the DOF change) then you
> will not sample the same states.
>
> Mark
>
> On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
>
> > Dear Mark,
> > thanks, but degrees of freedom goes to kinetic energies, still LJ
> energies
> > must be the same, yes?
> >
> >
> > Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Your systems have different available degrees of freedom, so they
> sample
> > > difference spaces. The energies you observe reflect that difference.
> > >
> > > Mark
> > >
> > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:
> > >
> > > > Hi,
> > > >
> > > > I have a system containing of a virtual site of carbon connected
> > > > symmetrically to two dummy massive sites (no charge). like :
> M---C---M
> > > > My problem is the results I get from simulation of this system is not
> > > equal
> > > > with results of single Carbon system simulation with mass of 2M (at
> > > exactly
> > > > similar conditions)?
> > > > They produce different LJ coul energies, I have even tried for
> > > non-charged
> > > > systems.
> > > >
> > > > Thank you in advance for help,
> > > > Best regards
> > > > --
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